CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies

Wood, C. W., Bruning, M., Ibarra, A. Á., Bartlett, G. J., Thomson, A. R. , Sessions, R. B., Brady, R. L. and Woolfson, D. N. (2014) CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies. Bioinformatics, 30(21), pp. 3029-3035. (doi:10.1093/bioinformatics/btu502) (PMID:25064570) (PMCID:PMC4201159)

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Abstract

Motivation: The ability to accurately model protein structures at the atomistic level underpins efforts to understand protein folding, to engineer natural proteins predictably and to design proteins de novo . Homology-based methods are well established and produce impressive results. However, these are limited to structures presented by and resolved for natural proteins. Addressing this problem more widely and deriving truly ab initio models requires mathematical descriptions for protein folds; the means to decorate these with natural, engineered or de novo sequences; and methods to score the resulting models. Results: We present CCBuilder, a web-based application that tackles the problem for a defined but large class of protein structure, the α-helical coiled coils. CCBuilder generates coiled-coil backbones, builds side chains onto these frameworks and provides a range of metrics to measure the quality of the models. Its straightforward graphical user interface provides broad functionality that allows users to build and assess models, in which helix geometry, coiled-coil architecture and topology and protein sequence can be varied rapidly. We demonstrate the utility of CCBuilder by assembling models for 653 coiled-coil structures from the PDB, which cover >96% of the known coiled-coil types, and by generating models for rarer and de novo coiled-coil structures. Availability and implementation: CCBuilder is freely available, without registration, at http://coiledcoils.chm.bris.ac.uk/app/cc_builder/

Item Type:Articles
Additional Information:C.W.W. thanks the BBSRC for a PhD studentship through the South West Doctoral Training Partnership. D.N.W. thanks the EPSRC (EP/J001430/1), BBSRC (BB/ J008990/1; grant with RLB) and the ERC (340764) for financial support.
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Thomson, Dr Drew
Authors: Wood, C. W., Bruning, M., Ibarra, A. Á., Bartlett, G. J., Thomson, A. R., Sessions, R. B., Brady, R. L., and Woolfson, D. N.
College/School:College of Science and Engineering > School of Chemistry
Journal Name:Bioinformatics
Publisher:Oxford University Press
ISSN:1367-4803
ISSN (Online):1460-2059
Published Online:26 July 2014
Copyright Holders:Copyright © 2014 The Authors
First Published:First published in Bioinformatics 30(21): 3029-3035
Publisher Policy:Reproduced under a Creative Commons License

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